The lasers are fired through three of the glass shafts emanating from the cube, but must be carefully directed out of the other side to prevent them scattering within the clock, which is why there are six shafts in total.

However:

… the beating heart of a time machine! Or “clock”, as most people call them …

… or possibly “frequency standard” as I like to pedantically point out. Though this being an ion clock, it can probably run for extended periods of time, and one might actually be able to say it’s running as a clock.

I also find the description of the six arms to be curious; normally, trapping schemes send light in both directions. It’s true you don’t want the light scattered in the chamber, but the description implies there are only three, and none of the NPL write-ups I have read say anything about a novel cooling geometry requiring only three beams.

Aaand it gives the Sr transition frequency as an exact number. There should be an uncertainty, since it’s the Cs hyperfine transition which is defined.